EM structure of Bacillus subtilis ribonucleotide reductase inhibited filament composed of NrdE alpha subunit and NrdF beta subunit with dATP

Experimental Data Snapshot

  • Resolution: 4.65 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

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This is version 1.2 of the entry. See complete history


Convergent allostery in ribonucleotide reductase.

Thomas, W.C.Brooks 3rd, F.P.Burnim, A.A.Bacik, J.P.Stubbe, J.Kaelber, J.T.Chen, J.Z.Ando, N.

(2019) Nat Commun 10: 2653-2653

  • DOI: https://doi.org/10.1038/s41467-019-10568-4
  • Primary Citation of Related Structures:  
    6MT9, 6MV9, 6MVE, 6MW3, 6MYX

  • PubMed Abstract: 

    Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, 97239, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductaseA [auth C],
B [auth D]
700Bacillus subtilisMutation(s): 0 
Gene Names: nrdE_1B4417_3413NCTC3610_03984
Find proteins for P50620 (Bacillus subtilis (strain 168))
Explore P50620 
Go to UniProtKB:  P50620
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50620
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleoside-diphosphate reductase NrdF beta subunitC [auth I],
D [auth J]
8Bacillus subtilisMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 4.65 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124847
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100008

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence, Other